Count yourself lucky that you may have a partial solution for your
structure with only 30% identity. The question now is: can you see any
reasonable, traceable electron density for domain A?
Cheers,
___
Roger S. Rowlett
Gordon Dorothy Kline Professor
The fact that you have a 10% split between R/Rfree means your solution is
heavily model biased (rule of thumb is a split of 5%). An Rfree of 0.55 would
imply randomness. So unfortunately in this case, I dont think that you have an
actual solution. You could try MR with a poly-A form of the
First of all, thanks so much for your reply.
To Roger:
NO, unfortunately I cannot see too much traceable electron density outside
the placed atoms, so I think just as Greg said, it's only a model-biased
solution.
To Greg:
YES, I also realized that the input model should be very important, so I'm
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Dear Zhihong,
in many labs a SeMet prep is not much effort and can be done within a
week or two, if you express in E.coli. Unless the costs are a limiting
factor I would certainly go this way. However, with native data to
3.5A I suggest you contact
Do you expect more than one molecule in the asymmetric unit?
Determined from the Matthews Coefficient (poor), size exclusion column
(better), or self RF (best) ?
On Nov 7, 2013, at 8:36 AM, Zhihong Yu nkyuz...@gmail.com wrote:
Hi, all
I'm a rookie in resolving a brand new structure. I
Thanks Francis,
No, only one molecule in the asu. The Matthews Coefficient is 3.3,
corresponding solvent content is 62.6%, maybe that's why this crystal show
such weak diffraction?
Zhihong
On Thu, Nov 7, 2013 at 5:37 PM, Francis Reyes francis.re...@colorado.eduwrote:
Do you expect more than
-optimal cases
Best,
Debanu.
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Zhihong Yu
[nkyuz...@gmail.com]
Sent: Thursday, November 07, 2013 2:53 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] few questions about resolving new
Dear CCP4 users,
I would like to draw your attention to the topic If it is a new
structure?, which is one more case, when new community members were
welcomed, and were gently explained about the rules of files sharing,
as it is an evidence, that the rules about files sharing are not well
Hi,
Last couple of times I asked myself the same question (what does it
look like?) I used ssm (or PDBeFold as seems to be called now).
http://www.ebi.ac.uk/msd-srv/ssm/
HTH,
Fred.
Liu Zhao wrote:
The structure of my protein is as shown as the purple one. Another one
,as shown as
You're welcome!
Next time, irrespective of whether your structure is a new one or not,
please upload your images to picasa, flickr, your university's file
sharing server or some such thing and include the link in your email.
Don't flood several thousand inboxes with megabytes of pixels. And
Hi Liu,
If I understand your question correctly, youre asking how different
do two structures need to be for one to be new'. If by new you
mean a new fold, then the answer is NO. Your structure and the homolog
have the same fold.
However, if your structure is the first structure of a
On 12/20/10 05:49, Liu Zhao wrote:
The structure of my protein is as shown as the purple one. Another one
,as shown as green,is homologous .But the structure of my protein
can't be obtained by using molecular replacement. And both structures
have much different, especially in B chain. If my
, 2010 8:57 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] If it is a new structure?
Hi Liu,
If I understand your question correctly, youre asking how different
do two structures need to be for one to be new'. If by new you
mean a new fold, then the answer is NO. Your structure
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